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  1. AU="Blackburne, Brittney"
  2. AU="Bortoleti, Bruna Taciane da Silva"
  3. AU="Ehrbar, Martin"
  4. AU="Lepre, Davide"
  5. AU="Olszewska, Zuzanna"
  6. AU="Vojta, Leslie"
  7. AU=Wickstrom Eric AU=Wickstrom Eric
  8. AU="Gangavarapu, Sridevi"
  9. AU="Hussein, Hazem Abdelwaheb"
  10. AU=Cai Yixin AU=Cai Yixin
  11. AU="Hüls, Anke"
  12. AU="Poondru, Srinivasu"
  13. AU="Coca, Daniel"
  14. AU="Lebeau, Paul"
  15. AU="Dehghani, Sedigheh"
  16. AU="Ishibashi, Kenji"
  17. AU="Xu, Yanhua"
  18. AU="Matera, Katarzyna"
  19. AU="Ait-Ouarab, Slimane"
  20. AU="Nicola, Coppede"
  21. AU="Dewitt, John M"
  22. AU="Sorin M. Dudea"
  23. AU="Tanusha D. Ramdin"
  24. AU="Hao, Zehui"
  25. AU="Chauhan, Aman"

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  1. Artikel: Acyl-CoA thioesterase-2 facilitates β-oxidation in glycolytic skeletal muscle in a lipid supply dependent manner.

    Bekeova, Carmen / Han, Ji In / Xu, Heli / Kerr, Evan / Blackburne, Brittney / Lynch, Shannon C / Mesaros, Clementina / Murgia, Marta / Vadigepalli, Rajanikanth / Beld, Joris / Leonardi, Roberta / Snyder, Nathaniel W / Seifert, Erin L

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Acyl-Coenzyme A (acyl-CoA) thioesters are compartmentalized intermediates that participate in in multiple metabolic reactions within the mitochondrial matrix. The limited availability of free CoA (CoASH) in the matrix raises the question of how the local ...

    Abstract Acyl-Coenzyme A (acyl-CoA) thioesters are compartmentalized intermediates that participate in in multiple metabolic reactions within the mitochondrial matrix. The limited availability of free CoA (CoASH) in the matrix raises the question of how the local acyl-CoA concentration is regulated to prevent trapping of CoASH from overload of any specific substrate. Acyl-CoA thioesterase-2 (ACOT2) hydrolyzes long-chain acyl-CoAs to their constituent fatty acids and CoASH, and is the only mitochondrial matrix ACOT refractory to inhibition by CoASH. Thus, we reasoned that ACOT2 may constitutively regulate matrix acyl-CoA levels.
    Sprache Englisch
    Erscheinungsdatum 2023-06-27
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.06.27.546724
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Phylogenomic analysis of the diversity of graspetides and proteins involved in their biosynthesis.

    Makarova, Kira S / Blackburne, Brittney / Wolf, Yuri I / Nikolskaya, Anastasia / Karamycheva, Svetlana / Espinoza, Marlene / Barry, Clifton E / Bewley, Carole A / Koonin, Eugene V

    Biology direct

    2022  Band 17, Heft 1, Seite(n) 7

    Abstract: Background: Bacteria and archaea produce an enormous diversity of modified peptides that are involved in various forms of inter-microbial conflicts or communication. A vast class of such peptides are Ribosomally synthesized, Postranslationally modified ... ...

    Abstract Background: Bacteria and archaea produce an enormous diversity of modified peptides that are involved in various forms of inter-microbial conflicts or communication. A vast class of such peptides are Ribosomally synthesized, Postranslationally modified Peptides (RiPPs), and a major group of RiPPs are graspetides, so named after ATP-grasp ligases that catalyze the formation of lactam and lactone linkages in these peptides. The diversity of graspetides, the multiple proteins encoded in the respective Biosynthetic Gene Clusters (BGCs) and their evolution have not been studied in full detail. In this work, we attempt a comprehensive analysis of the graspetide-encoding BGCs and report a variety of novel graspetide groups as well as ancillary proteins implicated in graspetide biosynthesis and expression.
    Results: We compiled a comprehensive, manually curated set of graspetides that includes 174 families including 115 new families with distinct patterns of amino acids implicated in macrocyclization and further modification, roughly tripling the known graspetide diversity. We derived signature motifs for the leader regions of graspetide precursors that could be used to facilitate graspetide prediction. Graspetide biosynthetic gene clusters and specific precursors were identified in bacterial divisions not previously known to encode RiPPs, in particular, the parasitic and symbiotic bacteria of the Candidate phyla radiation. We identified Bacteroides-specific biosynthetic gene clusters (BGC) that include remarkable diversity of graspetides encoded in the same loci which predicted to be modified by the same ATP-grasp ligase. We studied in details evolution of recently characterized chryseoviridin BGCs and showed that duplication and horizonal gene exchange both contribute to the diversification of the graspetides during evolution.
    Conclusions: We demonstrate previously unsuspected diversity of graspetide sequences, even those associated with closely related ATP-grasp enzymes. Several previously unnoticed families of proteins associated with graspetide biosynthetic gene clusters are identified. The results of this work substantially expand the known diversity of RiPPs and can be harnessed to further advance approaches for their identification.
    Mesh-Begriff(e) Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/metabolism ; Bacteria/genetics ; Multigene Family ; Peptides/chemistry ; Phylogeny ; Protein Processing, Post-Translational
    Chemische Substanzen Peptides ; Adenosine Triphosphate (8L70Q75FXE)
    Sprache Englisch
    Erscheinungsdatum 2022-03-21
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Intramural
    ZDB-ID 2221028-3
    ISSN 1745-6150 ; 1745-6150
    ISSN (online) 1745-6150
    ISSN 1745-6150
    DOI 10.1186/s13062-022-00320-2
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel: Structural Basis for a Dual Function ATP Grasp Ligase That Installs Single and Bicyclic ω-Ester Macrocycles in a New Multicore RiPP Natural Product

    Zhao, Gengxiang / Kosek, Dalibor / Liu, Hong-Bing / Ohlemacher, Shannon I / Blackburne, Brittney / Nikolskaya, Anastasia / Makarova, Kira S / Sun, Jiadong / Barry III, Clifton E / Koonin, Eugene V / Dyda, Fred / Bewley, Carole A

    Journal of the American Chemical Society. 2021 May 24, v. 143, no. 21

    2021  

    Abstract: Among the ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, “graspetides” (formerly known as microviridins) contain macrocyclic esters and amides that are formed by ATP-grasp ligase tailoring enzymes using the ... ...

    Abstract Among the ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, “graspetides” (formerly known as microviridins) contain macrocyclic esters and amides that are formed by ATP-grasp ligase tailoring enzymes using the side chains of Asp/Glu as acceptors and Thr/Ser/Lys as donors. Graspetides exhibit diverse patterns of macrocylization and connectivities exemplified by microviridins, that have a caged tricyclic core, and thuringin and plesiocin that feature a “hairpin topology” with cross-strand ω-ester bonds. Here, we characterize chryseoviridin, a new type of multicore RiPP encoded by Chryseobacterium gregarium DS19109 (Phylum Bacteroidetes) and solve a 2.44 Å resolution crystal structure of a quaternary complex consisting of the ATP-grasp ligase CdnC bound to ADP, a conserved leader peptide and a peptide substrate. HRMS/MS analyses show that chryseoviridin contains four consecutive five- or six-residue macrocycles ending with a microviridin-like core. The crystal structure captures respective subunits of the CdnC homodimer in the apo or substrate-bound state revealing a large conformational change in the B-domain upon substrate binding. A docked model of ATP places the γ-phosphate group within 2.8 Å of the Asp acceptor residue. The orientation of the bound substrate is consistent with a model in which macrocyclization occurs in the N- to C-terminal direction for core peptides containing multiple Thr/Ser-to-Asp macrocycles. Using systematically varied sequences, we validate this model and identify two- or three-amino acid templating elements that flank the macrolactone and are required for enzyme activity in vitro. This work reveals the structural basis for ω-ester bond formation in RiPP biosynthesis.
    Schlagwörter Chryseobacterium ; amides ; biosynthesis ; crystal structure ; enzyme activity ; ligases ; macrocyclization reactions ; models ; peptides ; signal peptide
    Sprache Englisch
    Erscheinungsverlauf 2021-0524
    Umfang p. 8056-8068.
    Erscheinungsort American Chemical Society
    Dokumenttyp Artikel
    Anmerkung NAL-AP-2-clean
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.1c02316
    Datenquelle NAL Katalog (AGRICOLA)

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  4. Artikel ; Online: Structural Basis for a Dual Function ATP Grasp Ligase That Installs Single and Bicyclic ω-Ester Macrocycles in a New Multicore RiPP Natural Product.

    Zhao, Gengxiang / Kosek, Dalibor / Liu, Hong-Bing / Ohlemacher, Shannon I / Blackburne, Brittney / Nikolskaya, Anastasia / Makarova, Kira S / Sun, Jiadong / Barry Iii, Clifton E / Koonin, Eugene V / Dyda, Fred / Bewley, Carole A

    Journal of the American Chemical Society

    2021  Band 143, Heft 21, Seite(n) 8056–8068

    Abstract: Among the ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, "graspetides" (formerly known as microviridins) contain macrocyclic esters and amides that are formed by ATP-grasp ligase tailoring enzymes using the ... ...

    Abstract Among the ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, "graspetides" (formerly known as microviridins) contain macrocyclic esters and amides that are formed by ATP-grasp ligase tailoring enzymes using the side chains of Asp/Glu as acceptors and Thr/Ser/Lys as donors. Graspetides exhibit diverse patterns of macrocylization and connectivities exemplified by microviridins, that have a caged tricyclic core, and thuringin and plesiocin that feature a "hairpin topology" with cross-strand ω-ester bonds. Here, we characterize chryseoviridin, a new type of multicore RiPP encoded by
    Mesh-Begriff(e) Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/metabolism ; Amides/chemistry ; Amides/metabolism ; Biological Products/chemistry ; Biological Products/metabolism ; Esters/chemistry ; Esters/metabolism ; Ligases/chemistry ; Ligases/metabolism ; Macrocyclic Compounds/chemistry ; Macrocyclic Compounds/metabolism ; Molecular Conformation ; Peptides/chemistry ; Peptides/metabolism ; Protein Processing, Post-Translational
    Chemische Substanzen Amides ; Biological Products ; Esters ; Macrocyclic Compounds ; Peptides ; Adenosine Triphosphate (8L70Q75FXE) ; Ligases (EC 6.-)
    Sprache Englisch
    Erscheinungsdatum 2021-05-24
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.1c02316
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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